Regulatory elements from labyrinthulomycetes microorganisms

Abstract

The present disclosure generally relates to novel polynucleotide molecules for use in regulating gene expression in recombinant cells, such as labyrinthulomycetes cells. The disclosure further relates to nucleic acid constructs, such as vectors and expression cassettes, containing a regulatory element operably linked to a heterologous nucleotide sequence. The disclosure further relates to methods for stably transforming a host cell, such as a labyrinthulomycetes cell with transgenes. Stably transformed recombinant cells, progeny, biomaterials derived therefrom, and methods for preparing and using the same are also provided.

What is claimed is: 
     
       1. A nucleic acid construct comprising a nucleic acid sequence that comprises a promoter, wherein the nucleic acid sequence exhibits at least 95% sequence identity to at least 650 contiguous nucleotides from the 3′ end of a nucleic acid sequence selected from the group consisting of SEQ ID NO:59, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:196, and SEQ ID NO:199;
 wherein the promoter is operably linked to a heterologous nucleic acid sequence. 
 
     
     
       2. The nucleic acid construct of  claim 1 , wherein said nucleic acid sequence exhibits at least 95% sequence identity to a nucleic acid sequence selected from the group consisting of SEQ ID NO:59, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:196, and SEQ ID NO:199. 
     
     
       3. The nucleic acid construct of  claim 1 , wherein the nucleic acid sequence exhibits at least 98% sequence identity to at least 650 contiguous nucleotides from the 3′ end of a nucleic acid sequence selected from the group consisting of SEQ ID NO:59, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:196, and SEQ ID NO:199. 
     
     
       4. The nucleic acid construct of  claim 3 , wherein the nucleic acid sequence exhibits at least 99% sequence identity to at least 650 contiguous nucleotides from the 3′ end of a nucleic acid sequence selected from the group consisting of SEQ ID NO:59, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:196, and SEQ ID NO:199. 
     
     
       5. The nucleic acid construct of  claim 1 , wherein the promoter is functional in a  Schizochytrium  or  Aurantiochytrium  cell. 
     
     
       6. The nucleic acid construct of  claim 1 , wherein said heterologous nucleic acid sequence encodes a polypeptide or a functional RNA. 
     
     
       7. The nucleic acid construct of  claim 6 , wherein said heterologous nucleic acid sequence encodes a functional RNA selected from: a ribosomal RNA, a tRNA, a ribozyme, a transactivating (tr) RNA of a CRISPR system, a crispr (cr) RNA of a CRISPR system, a chimeric guide RNA of a CRISPR system, a micro RNA, an interfering RNA (RNAi) molecule, a short hairpin (sh) RNA, or an antisense RNA molecule. 
     
     
       8. The nucleic acid construct of  claim 1 , wherein said heterologous nucleic acid sequence is operably linked to a terminator. 
     
     
       9. The nucleic acid construct of  claim 8 , wherein the terminator comprises a sequence having at least 90% sequence identity to a sequence selected from the group consisting of SEQ ID NOs:71-78. 
     
     
       10. The nucleic acid construct of  claim 1 , wherein the promoter is functional in a Labyrinthulomycetes cell. 
     
     
       11. The nucleic acid construct of  claim 6 , wherein said construct is further defined as an expression cassette or a vector. 
     
     
       12. The nucleic acid construct of  claim 6 , wherein the heterologous nucleic acid sequence encodes a transcription factor, DNA binding protein, splicing factor, nuclease, a cas protein, a recombinase, a G protein, a nucleotide cyclase, a phosphodiesterase, a kinase, a polypeptide of that participates in protein secretion or protein trafficking, a structural protein, a hormone, a cytokine, an antibody, a transporter, an enzyme having lypolytic activity, a thioesterase, an amidase, a lipase, a fatty acid synthase or a component of a fatty acid synthase complex, a pfaA, pfaB, pfaC, pfaD, or pfaE polypeptide, an acyl-CoA synthetase, an acyl-ACP synthetase, an acyl carrier protein, an acyl-CoA carboxylase, an acyl transferase, an enzyme that participates in glycolysis, a dehydrogenase, an enzyme of the TCA cycle, a fatty acid desaturase, or a fatty acid elongase. 
     
     
       13. The nucleic acid construct of  claim 6 , wherein said heterologous nucleic acid sequence comprises a selectable marker or a reporter gene. 
     
     
       14. The nucleic construct of  claim 13 , wherein said selectable marker gene is selected from the group consisting of a gene conferring resistance to an antibiotic, a gene conferring resistance to an herbicide, a gene encoding acetyl CoA carboxylase (ACCase), a gene encoding acetohydroxy acid synthase (ahas), a gene encoding acetolactate synthase, a gene encoding aminoglycoside phosphotransferase, a gene encoding anthranilate synthase, a gene encoding bromoxynil nitrilase, a gene encoding cytochrome P450-NADH-cytochrome P450 oxidoreductase, a gene encoding dalapon dehalogenase, a gene encoding dihydropteroate synthase, a gene encoding a class I 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), a gene encoding a class II EPSPS (aroA), a gene encoding a non-class I II EPSPS, a gene encoding glutathione reductase, a gene encoding glyphosate acetyltransferase, a gene encoding glyphosate oxidoreductase, a gene encoding hydroxyphenylpyruvate dehydrogenase, a gene encoding hydroxy-phenylpyruvate dioxygenase, a gene encoding isoprenyl pyrophosphate isomerase, a gene encoding lycopene cyclase, a gene encoding phosphinothricin acetyl transferase, a gene encoding phytoene desaturase, a gene encoding prenyl transferase, a gene encoding protoporphyrin oxidase, a gene encoding superoxide dismutase, arg7, his3, hisD, hisG, manA, nitl, trpB, uidA, xylA, a dihydrofolate reductase gene, a mannose-6-phosphate isomerase gene, a nitrate reductase gene, an ornithine decarboxylase gene, a thymidine kinase gene, a 2-deoxyglucose resistance gene; and an R-locus gene. 
     
     
       15. A method of transforming a eukaryotic cell, comprising:
 (i) introducing into a eukaryotic cell the nucleic acid construct of  claim 6 ; and 
 (ii) selecting or screening for a transformed eukaryotic cell. 
 
     
     
       16. A method according to  claim 15 , wherein the nucleic acid molecule is introduced by a biolistic procedure or electroporation. 
     
     
       17. A recombinant cell comprising the nucleic acid construct of  claim 1 . 
     
     
       18. The recombinant cell of  claim 17 , wherein said nucleic acid construct is stably integrated into the genome of said recombinant cell. 
     
     
       19. The recombinant cell of  claim 17 , wherein the recombinant cell belongs to the class Labyrinthulomycetes. 
     
     
       20. The recombinant cell of  claim 19 , wherein said labyrinthulomycetes microorganism is an  Aplanochytrium , an  Aurantiochytrium , a  Diplophrys , a  Japonochytrium , an  Oblongichytrium , a  Schizochytrium , a  Thraustochytrium , or an  Ulkenia  microorganism. 
     
     
       21. The nucleic acid construct of  claim 1 , wherein said nucleic acid sequence exhibits at least 95% sequence identity to: at least 800 contiguous nucleotides from the 3′ end of the nucleic acid sequence of SEQ ID NO:196 or at least 800 contiguous nucleotides from the 3′ end of the nucleic acid sequence of SEQ ID NO:199.